CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini

Wang, Heming; Huang, Rong; Li, Ling; Zhu, Junjin; Li, Zhihong; Peng, Chao; Zhuang, Xuran; Lin, Haifan; Shi, Shuo; Huang, Pengyu

doi:10.1038/s41421-021-00265-2

Cited by 41 publications

(52 citation statements)

References 51 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Such comparison provides us the information what proportion of RNA species we profiled is 3′-cP/P-terminated or 3′-OH-terminated. This information could not be provided by other methods, including tRNA-seq (Ma et al, 2021;Zheng et al, 2015), PANDORA-seq (Shi et al, 2021) and CPA-seq (Wang et al, 2021a) even though these methods can capture RNA species with different termini. For analysis of 3′-cP-terminated RNAs alone, RtcB sRNA-seq has a reduced number of steps for library construction and is time-saving, compared with cP-sRNA-seq (Honda et al, 2015;Honda et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…For example, methylation severely blocks reverse transcription. Demethylation enzymes have been used to remove RNA methylation to facilitate reverse transcription in tRNA-seq (Cozen et al, 2015;Ma et al, 2021;Zheng et al, 2015), PANDORA-seq (Shi et al, 2021) and CPA-seq (Wang et al, 2021a). We did not use enzymes to remove modifications before RtcB sRNA-seq.…”

Section: Discussionmentioning

confidence: 99%

“…Like tRNAs, tsRNAs carry a plethora of post-transcriptional modifications. Conventional sRNA-seq that only captures sRNAs with 3′ OH (Alves et al, 2017;Cognat et al, 2017;Martinez et al, 2017), cP-RNA-seq that only captures 3′-cP-terminated RNAs (Honda et al, 2015;Honda et al, 2016), tRNA-seq, panoramic RNA display by overcoming RNA modification aborted sequencing (PANDORA-seq) and small ncRNA sequencing (CPAseq) that recover sRNAs with different termini and nucleoside methylation (Cozen et al, 2015;Ma et al, 2021;Shi et al, 2021;Wang et al, 2021a;Zheng et al, 2015) have been developed to identify RNAs with different termini and modifications and led to the discovery of a large number of tsRNAs in mammals and plants.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

A 5′ tRNA-Ala-derived small RNA regulates anti-fungal defense in plants

Yuan

et al. 2021

Sci. China Life Sci.

View full text Add to dashboard Cite

Apart from their primordial role in protein synthesis, tRNAs can be cleaved to produce tRNA-derived small RNAs (tsRNAs). The biological functions of tsRNAs in plants remain largely unknown. In this study, we developed RtcB ligation-based small RNA (sRNA) sequencing, a method that captures and distinguishes between 3′-2′,3′-cyclic-phosphate (cP)/phosphate (P)terminated sRNAs and 3′-OH-terminated sRNAs, and profiled 5′ tsRNAs and 5′ tRNA halves in Arabidopsis thaliana. We found that Arabidopsis 5′ tsRNAs and 5′ tRNA halves predominantly contain a cP at the 3′ end and require S-like RNase 1 (RNS1) and RNS3 for their production. One of the most abundant 5′ tsRNAs, 5′ tsR-Ala, by associating with AGO1, negatively regulates Cytochrome P450 71A13 (CYP71A13) expression and camalexin biosynthesis to repress anti-fungal defense. Interestingly, 5′ tsR-Ala is downregulated upon fungal infection. Our study provides a global view of 5′ tsRNAs and 5′ tRNA halves in Arabidopsis and unravels an important role of a 5′ tsRNA in regulating anti-fungal defense.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

A 5′ tRNA-Ala-derived small RNA regulates anti-fungal defense in plants

Yuan

et al. 2021

Sci. China Life Sci.

View full text Add to dashboard Cite

show abstract

“…The total RNA of the tissues for sequencing was pretreated to remove some RNA modifications. The following experiments were carried out to remove some RNA modifications that may disturb small RNA-sequencing library construction ( 28 , 29 ): 3′-aminoacyl (charged) deacylation to 3′-OH (hydroxyl group) for 3′ adaptor ligation, 3′-cP (2′, 3′-cyclic phosphate) removal to 3′-OH for 3′ adaptor ligation, 5′-OH phosphorylation to 5′-P for 5′-adaptor ligation, and N1-methyladenosine and N3-methylcytidine demethylation for efficient reverse transcription. All methods were conducted based on the rtStar tRF&tiRNA Pretreatment Kit (Arraystar, USA) protocols.…”

Section: Methodsmentioning

confidence: 99%

Altered Expression of Transfer-RNA-Derived Small RNAs in Human With Rheumatic Heart Disease

Yang

et al. 2021

Front. Cardiovasc. Med.

View full text Add to dashboard Cite

Rheumatic heart disease (RHD) remains a severe public health problem in developing countries. Atrial fibrillation (AF) is a medical complication of RHD. Although the understanding of disease pathogenesis has advanced in recent years, the key questions need to be addressed. Transfer RNA–derived small RNAs (tsRNAs) are a novel type of short non-coding RNAs with potential regulatory functions in various physiological and pathological processes. The present study used tsRNAs sequencing to investigate the relationship between RHD and atrial fibrillation (AF). Three paired cardiac papillary muscles were taken from six rheumatic RHD patients with AF (3 cases) or without AF (3 cases) from January 2016 to January 2017 in Xiangya Hospital, Central South University. A total of 219 precisely matched tsRNAs were identified, and 77 tsRNAs (fold change > 2.0 and P < 0.05) were differently changed. Three tsRNAs (AS-tDR-001269, AS-tDR-001363, AS-tDR-006049) were randomly selected and confirmed by qRT-PCR. The results of qRT-PCR were consistent with tsRNAs sequencing, suggesting the tsRNAs sequencing was reliable. Subsequently, we predicted the target mRNAs of the three tsRNAs. Moreover, we verified the functions of tsRNAs targeting mRNAs in vitro. Finally, bioinformatics analysis indicated that the target genes were abundant in regulation of transcription, DNA binding, intracellular. Most of the genes were predicted to interplay with cytokine-cytokine receptor by KEGG analysis. Our findings uncover the pathological process of AF in RHD through tsRNAs sequencing. This research provides a new perspective for future research on elucidating the mechanism of AF in RHD and offers potential new candidates for the treatment and diagnosis.

show abstract

“…Emerging studies elucidated that tsRNAs take an important part in post-transcriptional regulation [ [111] , [112] , [113] , [114] ]. Ranging from prokaryotes to eukaryotes, many tsRNAs have been discovered in diverse species with the advent of deep-sequencing [ [115] , [116] , [117] ]. Originating from mature tRNAs or precursor tRNAs, tsRNAs play distinct roles in various biological processes, including interactions with proteins or RNAs, translation inhibition, chromatin regulation, and epigenetic modifications [ 118 , 119 ].…”

Section: Chemical Modifications In Tsrnamentioning

confidence: 99%

The epitranscriptome of small non-coding RNAs

2021

Non-coding RNA Research

View full text Add to dashboard Cite

Small non-coding RNAs are short RNA molecules and involved in many biological processes, including cell proliferation and differentiation, immune response, cell death, epigenetic regulation, metabolic control. A diversity of RNA modifications have been identified in these small non-coding RNAs, including transfer RNAs (tRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small nuclear RNA (snRNA), small nucleolar RNAs (snoRNAs), and tRNA-derived small RNAs (tsRNAs). These post-transcriptional modifications are involved in the biogenesis and function of these small non-coding RNAs. In this review, we will summarize the existence of RNA modifications in the small non-coding RNAs and the emerging roles of these epitranscriptomic marks.

show abstract

CPA-seq reveals small ncRNAs with methylated nucleosides and diverse termini

Cited by 41 publications

References 51 publications

A 5′ tRNA-Ala-derived small RNA regulates anti-fungal defense in plants

A 5′ tRNA-Ala-derived small RNA regulates anti-fungal defense in plants

Altered Expression of Transfer-RNA-Derived Small RNAs in Human With Rheumatic Heart Disease

The epitranscriptome of small non-coding RNAs

Contact Info

Product

Resources

About